The paper introduces SM3DD, a 3D spatial transcriptomics analysis method, and finds differences in transcript distances between normal and SARS-CoV-2 patient lung tissues.

NAR Genomics and Bioinformatics · Jan 6, 2026Peer-reviewedBioinformatics

PRISM: A Python Package for Interactive and Integrated Analysis of Multiplexed Tissue Microarrays

Rafael Tubelleza, Aaron Kilgallon, Chin Wee Tan, James H. Monkman, John Francis Fraser, Arutha Kulasinghe

PRISM is a Python package for interactive analysis of multiplexed tissue microarrays, enabling translational and clinical research using spatial proteomic data from multiple platforms.

NAR Genomics and Bioinformatics · Jul 4, 2025Peer-reviewedBioinformatics

Whole transcriptome profiling of placental pathobiology in SARS-CoV-2 pregnancies identifies placental dysfunction signatures

Nataly Stylianou, Ismail Sebina, Nicholas Matigian, James H. Monkman, Hadeel Doehler, Joan Röhl, Mark C. Allenby, Andy Nam, Liuliu Pan, Anja Rockstroh, Habib Sadeghirad, Kimberly Chung, Thais Sobanski, Kenneth John O'Byrne, Ana Clara Simoes Florido Almeida, , Arutha Kulasinghe

This study uses spatial transcriptomics to identify placental dysfunction signatures in SARS-CoV-2 infected pregnancies, revealing altered gene expression related to hypoxia, oxidative stress, and preeclampsia-like pathways.

Clinical & Translational Immunology · Jan 1, 2024Peer-reviewedDevelopmental Biology

A robust Platform for Integrative Spatial Multi-omics Analysis to Map Immune Responses to SARS-CoV-2 infection in Lung Tissues

Xiao Tan, Laura F. Grice, Minh Tran, Onkar Mulay, James H. Monkman, Tony Blick, Tuan Vo, Ana Clara Almeida, Jarbas da Silva Motta, Karen Fernandes de Moura, Cleber Machado Souza, Paulo Souza‐Fonseca‐Guimaraes, Cristina Pellegrino Baena, Lúcia de Noronha, Fernanda Simoes Fortes Guimaraes, , Quan Hoang Nguyen

This paper develops a spatial multi-omics platform to analyze immune responses in SARS-CoV-2-infected lung tissues, revealing macrophage infiltration and spatial heterogeneity in cytokine and interferon signaling.

Immunology · Aug 21, 2023Peer-reviewedBioinformatics